galaxyproject · bgruening · Aug 26, 2024 · Aug 18, 2024
@@ -0,0 +1,9 @@
+name: ucsc_chainsort
+owner: iuc
+description: Sort chains. By default sorts by score.
+long_description: Note this loads all chains into memory, so it is not suitable for large sets.  Instead, run chainSort on multiple small files, followed by chainMergeSort.
+homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort
+type: unrestricted
+categories:
+  - Sequence Analysis
@@ -0,0 +1,55 @@
+<tool id="ucsc_chainsort" name="chainSort" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        Sort chains
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">455</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-chainsort</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    chainSort
+        '$in_chain'
+        $sort_by
+        '$out'
+    ]]></command>
+    <inputs>
+        <param name="in_chain" format="chain" type="data" label="Chain dataset" />
+        <param name="sort_by" type="select" label="Sort">
+            <option value="" selected="true">by score</option>
+            <option value="-target">on target start</option>
+            <option value="-query">on query start</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out" format="chain" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_chain" value="input.chain" />
+            <output name="out" file="sorted_score.chain" />
+        </test>
+        <test>
+            <param name="in_chain" value="input.chain" />
+            <param name="sort_by" value="-query" />
+            <output name="out" file="sorted_query.chain" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`chainSort`_ is a tool to sort chains.
+
+Note this tool loads all chains into memory, so it is not suitable for large datasets. Instead, run chainSort on multiple small dataset, followed by chainMergeSort.
+
+.. _chainSort: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>
@@ -0,0 +1,150 @@
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+##gapPenalties=axtChain O=400 E=30
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